Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer

Anti-PD1 prolongs the response of PI3K and farnesyl transferase inhibition in HRAS- and PIK3CA-mutant head and neck cancers

BACKGROUND

Tipifarnib, a farnesyl transferase inhibitor, has shown promising response in the treatment of HRAS-mutant HNSCC in the clinic, and in combination with a PI3K inhibitor in PIK3CA-mutant mouse models; however, the involvement of antitumor immunity in the efficacy of tipifarnib has not yet been investigated. This study aimed to evaluate the involvement of antitumor immunity in the efficacy of tipifarnib in HRAS- or PIK3CA-mutant HPV-positive and HPV-negative head and neck cancer murine models.

METHODS

To investigate the role of antitumor immunity, we compared the efficacy of tipifarnib in immune-intact C57BL/6 mice and immunodeficient NSG mice. Histopathological analyses were conducted to evaluate PD-L1 expression and the activation of key signaling pathways. Additionally, the synergistic potential of tipifarnib with the PI3Kα inhibitor alpelisib (BYL719) was assessed in vitro and in vivo. Immunohistochemical analysis was performed to examine the infiltration of CD8+T cells, and anti-PD1 treatment was tested to evaluate its potential to prolong progression-free survival.

RESULTS

In the HPV-positive HRAS-mutant HNSCC model, the antitumor efficacy of tipifarnib was primarily dependent on CD8+T cell activity, whereas in HPV-negative cancers, the contribution of antitumor immunity was less pronounced. Tipifarnib treatment upregulated PD-L1 expression, potentially inhibiting T cell antitumor activity and inducing hyperactivation of the AKT pathway, which mitigated MAPK inhibition and promoted cell proliferation. Blocking the PI3K pathway with alpelisib demonstrated synergistic antitumor effects in all models. The combination of tipifarnib and alpelisib exhibited greater efficacy in immune-intact mice than in immunodeficient mice, and was accompanied by increased CD8+T cell infiltration. Adding anti-PD1 treatment to the tipifarnib/alpelisib combination further prolonged progression-free survival in tumor-bearing mice.

CONCLUSION

These findings underscore the critical role of antitumor immunity, particularly CD8+T cell activity, in the efficacy of tipifarnib alone and in combination with alpelisib. The triple combination of tipifarnib, alpelisib, and anti-PD1 treatment showed superior antitumor activity and extended survival in preclinical models, suggesting its potential as a therapeutic strategy for HNSCC patients with HRAS- and PIK3CA-mutation.

Salivary biomarkers: a promising approach for predicting immunotherapy response in head and neck cancers

Head and neck cancers, including cancers of the mouth, throat, voice box, salivary glands, and nose, are a significant global health issue. Radiotherapy and surgery are commonly used treatments. However, due to treatment resistance and disease recurrence, new approaches such as immunotherapy are being explored. Immune checkpoint inhibitors (ICIs) have shown promise, but patient responses vary, necessitating predictive markers to guide appropriate treatment selection. This study investigates the potential of non-invasive biomarkers found in saliva, oral rinses, and tumor-derived exosomes to predict ICI response in head and neck cancer patients. The tumor microenvironment significantly impacts immunotherapy efficacy. Oral biomarkers can provide valuable information on composition, such as immune cell presence and checkpoint expression. Elevated tumor mutation load is also associated with heightened immunogenicity and ICI responsiveness. Furthermore, the oral microbiota may influence treatment outcomes. Current research aims to identify predictive salivary biomarkers. Initial studies indicate that tumor-derived exosomes and miRNAs present in saliva could identify immunosuppressive pathways and predict ICI response. While tissue-based markers like PD-L1 have limitations, combining multiple oral fluid biomarkers could create a robust panel to guide treatment decisions and advance personalized immunotherapy for head and neck cancer patients.

Plac1+ Tumor Cell-Treg Interplay Supports Tumorigenesis and Progression of Head and Neck Cancer

Cancer/testis antigen (CTA) family is restricted to germline and tumor cells and plays an important role during cancer initiation and progression. Five single-cell and two bulk RNA-seq datasets are integrated to screen genes in the CTAs family, revealing that Placenta specific protein 1 (Plac1) is specifically expressed in head and neck squamous cell carcinoma (HNSCC) cells. Sp1 Transcription (SP1) is identified as a specific regulator of Plac1, which is confirmed by cleavage under targets and tagmentation (CUT&Tag)-seq. With in vitro experiments, in vivo subcutaneous tumor, and a transgenic autochthonous tumor model, it is revealed that Plac1 expression promotes HNSCC progression by inducing epidermal growth factor receptor endocytosis and recycling to increase PI3K/AKT signaling pathway activity. Then, it is revealed that Plac1+ tumor cells recruit CD4+ T cells via CXCL11/CXCR3 and induce Treg differentiation via PVR/TIGIT, which in turn activates the tumorigenic signaling of Plac1+ tumor cells via LTA/LTBR and forms a reciprocal protumor loop. These findings provide insights into molecular features of CTAs in HNSCC and facilitate the development of personalized treatment strategies.

Heterogeneity of the tumor immune cell microenvironment revealed by single-cell sequencing in head and neck cancer

Head and neck cancer (HNC) is the sixth most common disease in the world. The recurrence rate of patients is relatively high, and the heterogeneity of tumor immune microenvironment (TIME) cells may be an important reason for this. Single-cell sequencing (SCS) is currently the most promising and mature application in cancer research. It can identify unique genes expressed in cells and study tumor heterogeneity. According to current research, the heterogeneity of immune cells has become an important factor affecting the occurrence and development of HNC. SCSs can provide effective therapeutic targets and prognostic factors for HNC patients through analyses of gene expression levels and cell heterogeneity. Therefore, this study analyzes the basic theory of HNC and the development of SCS technology, elaborating on the application of SCS technology in HNC and its potential value in identifying HNC therapeutic targets and biomarkers.

Integrated multi-omics reveal lactate metabolism-related gene signatures and PYGL in predicting HNSCC prognosis and immunotherapy efficacy

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) treatment faces significant clinical challenges. Lactate metabolism plays a crucial role in the initiation of many cancers and the tumor microenvironment (TME). However, the prognostic significance of lactate metabolism-related genes (LMRGs) and the role of TME in HNSCC require further elucidation.

METHODS

We built a prognostic multigene signature with LMRGs and systematically correlated the risk signature with immunological characteristics and immunotherapy efficacy. Next, a series of single-cell sequencing analyses were used to characterize lactate metabolism in TME. Finally, single-cell sequencing analysis, immunofluorescence analyses, and a series of in vitro experiments were used to explore the role of PYGL in HNSCC. Potential drugs targeting PYGL were screened using AutoDock 4.2.

RESULTS

A prognostic multigene signature based on LMRGs was developed, which effectively stratified patients into high- and low-risk groups, with significant differences in overall survival (OS) and progression-free survival (PFS). Patients in the low-risk group exhibited reduced lactate metabolism, higher CD8 + T cell infiltration, and improved response to immunotherapy. Single-cell sequencing revealed that tumor cells had the most active lactate metabolism compared to other cells in the TME. PYGL, identified as the most critical prognostic gene, was highly expressed in tumor-associated macrophages and played a role in inhibiting M1 macrophage polarization. Knockdown of PYGL led to reduced lactate levels, and its expression was inversely correlated with CD8 + T cell infiltration. Furthermore, PYGL was involved in copper-dependent cell death, highlighting its potential as a therapeutic target. Drug screening identified elesclomol, which showed promising results in PYGL-knockdown cells.

CONCLUSIONS

The study established a robust LMRGs-based prognostic model that not only predicts patient survival but also correlates with the immune microenvironment in HNSCC. PYGL emerged as a key biomarker with significant implications for both prognosis and therapeutic intervention. Its role in regulating lactate metabolism and immune suppression suggests that targeting PYGL could enhance the efficacy of immunotherapies. This research provides a foundation for future clinical strategies aimed at improving outcomes in HNSCC by modulating the tumor's metabolic and immune landscapes.

A cohort of highly activated CD99- CD72+ B cells promoting autoimmune progression in juvenile systemic lupus erythematosus

CD72 inhibits the development of systemic lupus erythematosus (SLE) by suppressing TLR7-dependent B cell responses to self-nucleic acids (NAs). The absence of CD72 promotes the progression of lupus disease. Here, we find a highly activated subset of CD99- CD72+ B cells (CD72+ BCs) expressing elevated levels of TLR7 in juvenile SLE, which contributes to autoimmunity. Through multi-omics integrated analysis of single-cell RNA sequencing(scRNA-seq) data and bulk RNA sequencing (RNA-seq) data, we demonstrate that CD72+ BCs possess characteristics of both activated naïve B cells (aN) and age-associated B cells (ABCs). Concurrently, CD72+ BCs exhibit pronounced plasmablast-like features compared to other cellular subpopulations. We propose a plausible conclusion that CD72+ BCs represent a critical transitional cell population involved in the activation and subsequent plasma cell differentiation of naïve B cells and age-related B cells following exposure to self-antigens in SLE. This finding offers novel opportunities for elucidating the genesis of autoantibody-secreting cells involved in the autoimmune response processes in lupus.

Immunotherapeutic strategies in head and neck cancer: challenges and opportunities

HNSCC remains a substantial health issue, with treatment options including surgery, radiation, and platinum-based chemotherapy. Unfortunately, despite progress in research, only modest gains have been made in disease control, with existing treatments resulting in significant functional and quality-of-life issues. The introduction of immunotherapy in the treatment of HNSCC has resulted in some improvements in outlook for patients and is now standard of care for populations with both recurrent and metastatic disease. However, despite the early successes, responses to immune checkpoint inhibition (ICI) remain modest to low, approaching 14%-22% objective response rates. Challenges to the effectiveness of ICI and other immunotherapies are complex, including the diverse and dynamic molecular plasticity and heterogeneity of HNSCCs; lack of immunogenic antigens; accumulated suppressive immune populations such as myeloid cells and dysfunctional T cells; nutrient depletion; and metabolic dysregulation in the HNSCC tumor microenvironment. In this Review, we explore the mechanisms responsible for immunotherapy resistance, dissect these challenges, and discuss potential opportunities for overcoming hurdles to the development of successful immunotherapy for HNSCC.

Distinct CD8+ T cell dynamics associate with response to neoadjuvant cancer immunotherapies

We leverage a clinical trial (NCT04080804) that compared neoadjuvant anti-PD-1, anti-PD-1+CTLA-4, and anti-PD-1+LAG-3 therapies in head and neck squamous cell carcinoma patients. Combination therapies promote higher pathologic response rates versus monotherapy, and major pathologic response is associated with better survival. To address whether successful immune checkpoint inhibitor (ICI) regimens act through similar or distinct pathways, we robustly and longitudinally characterize transcriptional and proteomic dynamics of CD8+ tumor-infiltrating lymphocytes (TILs) in a clonal manner. Anti-PD-1+LAG-3 reprograms CD8+ TIL with type-I interferon response and exhaustion gene programs into effector memory and resident memory (TEM/TRM). In contrast, anti-PD-1+CTLA-4 activates and expands pre-existing TEM/TRM CD8+ TIL, but does not rejuvenate exhausted phenotypes into T effector cells. Anti-PD-1+LAG-3, but not anti-PD-1+CTLA-4, induces widespread TCR sharing among the different transcriptional states, as well as increased TCR diversity in responding patients. Our data suggest doublet regimen-specific transcriptional and clonal dynamics of tumor-reactive CD8+ T cells.

Mapping immunotherapy potential: spatial transcriptomics in the unraveling of tumor-immune microenvironments in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) often exhibits poor response rates to immune checkpoint inhibitor (ICI) therapies, largely owing to the intricate composition and spatial organization of immune cells within the tumor-immune microenvironment (TIME). The diversity of immune cell populations, their spatial relationships, and dynamic interactions significantly influence the immunosuppressive nature of the TIME, thereby limiting the efficacy of immunotherapy. To address these challenges and enhance the therapeutic potential of ICIs in HNSCC, a comprehensive analysis of the TIME is essential. Spatial transcriptomics (ST), a cutting-edge technology, enables high-resolution mapping of gene expression within the spatial context of the tumor, providing critical insights into the functional roles and interactions of immune cells in the TIME. This review highlights the importance of ST in uncovering the complexities of the TIME in HNSCC and proposes strategies for leveraging these insights to develop more effective immunotherapeutic approaches. By integrating spatial and molecular information, this review aims to pave the way for personalized and precision-based treatments in HNSCC, ultimately improving patient outcomes.

Glucose deprivation and identification of TXNIP as an immunometabolic modulator of T cell activation in cancer

Background

The ability of immune cells to rapidly respond to pathogens or malignant cells is tightly linked to metabolic pathways. In cancer, the tumor microenvironment (TME) represents a complex system with a strong metabolism stress, in part due to glucose shortage, which limits proper T cell activation, differentiation and functions preventing anti-tumor immunity.

Methods

In this study, we evaluated T cell immune reactivity in glucose-restricted mixed lymphocyte reaction (MLR), using a comprehensive profiling of soluble factors, multiparametric flow cytometry and single cell RNA sequencing (scRNA-seq).

Results

We determined that glucose restriction potentiates anti-PD-1 immune responses and identified thioredoxin-interacting protein (TXNIP), a negative regulator of glucose uptake, as a potential immunometabolic modulator of T cell activation. We confirmed TXNIP downregulation in tumor infiltrating T cells in cancer patients. We next investigated the implication of TXNIP in modulating immune effector functions in primary human T cells and showed that TXNIP depletion increased IFN-γ secretion and tumor cell killing.

Conclusions

TXNIP is at the interface between immunometabolism and T cell activation and could represent a potential target for immuno-oncology treatments.

Causal role of immune cells in thyroid cancer: a two-sample Mendelian randomization study

BACKGROUND

Immune cells play a crucial role in the progression of thyroid cancer. However, previous research on the link between immune cells and thyroid cancer has produced conflicting results.

METHODS

Based on the public available genome-wide association studies summary statistics, we performed a two-sample Mendelian randomization (MR) to evaluate the causal association between 731 immune phenotypes (including median fluorescence intensities, absolute cell counts, relative cell counts, and morphological parameters) and thyroid cancer. The inverse variance weighting method was employed to investigate the causal relationship between exposure and outcome. Moreover, multiple sensitivity analyses, such as MR-Egger, weighted median, and MR-PRESSO, were simultaneously applied to reinforce the final results.

RESULTS

After false discovery rate correction, four immunophenotypes were found to be significantly associated with a decreased risk of thyroid cancer. And six immunophenotypes were significantly associated with an increased risk of thyroid cancer.

CONCLUSIONS

Our study has demonstrated the close connection between immune cells and thyroid cancer by genetic means, thus providing guidance for future clinical research.

Overcoming immunotherapy resistance in hepatocellular carcinoma by targeting myeloid IL-8/CXCR2 signaling

Durable responses to immune checkpoint blockade (ICB) in hepatocellular carcinoma (HCC) are limited to a minority of patients, yet reliable biomarkers are still lacking. Inflammatory cytokines such as interleukin-8 (IL-8) are associated with HCC progression, and IL-8 is known as the chemoattractant for immunosuppressive myeloid cells. Therefore, we aim to elucidate the ICB resistance mechanisms mediated by the activation of the IL-8/CXCR2 pathway. Single-cell RNA sequencing (scRNA-seq) was performed in advanced HCC patients with baseline and on-treatment biopsy after pembrolizumab in a phase 2 clinical trial cohort. Our data revealed that IL-8 and its receptor, CXCR2, mainly derived from immunosuppressive myeloid-derived suppressor cells (MDSCs). In particular, the high circulating IL-8 level was strongly associated with poor ICB response. This myeloid IL-8/CXCR2 pathway was further elucidated in our ICB-resistant orthotopic mouse model using AZD5069, a clinically available CXCR2 antagonist. Suppression of the IL-8/CXCR2 pathway significantly abrogated MDSC trafficking and immunosuppressive activity, which sensitized the anti-PD-L1 blockade to reduce tumor growth and prolong survival. The association between myeloid IL-8 and ICB therapeutic outcomes also extended to multiple cancer types. Collectively, our study not only suggests a potential non-invasive biomarker for patient stratification and monitoring of ICB response but it also provides a proof of concept for combinational immunotherapy to benefit patients who are non-responsive to ICB monotherapy.

Vps34-orchestrated lipid signaling processes regulate the transitional heterogeneity and functional adaptation of effector regulatory T cells

Regulatory T cell (Treg) heterogeneity exists in lymphoid and non-lymphoid tissues, but we have limited understanding of context-dependent functions and spatiotemporal regulators of heterogenous Treg states, especially during perinatal life when immune tolerance is established. Here, we revealed that the class III PI3K Vps34 orchestrates effector Treg (eTreg) transitional heterogeneity during perinatal life. We found that loss of Vps34 reduced terminal eTreg accumulation in lymphoid tissues, associated with decreased Treg generation in non-lymphoid tissues and development of an early-onset autoimmune-like disease. After perinatal life, Vps34-deficient eTreg accumulation was further impaired due to reduced cell survival, highlighting temporal regulation of eTreg heterogeneity and maintenance by Vps34. Accordingly, inhibition of Vps34 in mature Tregs disrupted immune homeostasis but boosted anti-tumor immunity. Mechanistically, multiomics profiling approaches uncovered that Vps34-orchestrated transcriptional and epigenetic remodeling promotes terminal eTreg programming. Further, via genetic deletion of the Vps34-interacting proteins Atg14 or Uvrag in Tregs, we established that Atg14 but not Uvrag was required for the overall survival, but not terminal differentiation, of eTregs, suggesting that autophagy but not endocytosis partly contributed to Vps34-dependent effects. Accordingly, mice with Treg-specific loss of Atg14, but not Uvrag, had moderately disrupted immune homeostasis and reduced tumor growth, with Vps34- or Atg14-dependent gene signatures also being elevated in intratumoral Tregs from human cancer patients. Collectively, our study reveals distinct Vps34-orchestrated signaling events that regulate eTreg heterogeneity and functional adaptation and the pathophysiological consequences on autoimmunity versus anti-tumor immunity.

Machine Learning-Enabled Drug-Induced Toxicity Prediction

Unexpected toxicity has become a significant obstacle to drug candidate development, accounting for 30% of drug discovery failures. Traditional toxicity assessment through animal testing is costly and time-consuming. Big data and artificial intelligence (AI), especially machine learning (ML), are robustly contributing to innovation and progress in toxicology research. However, the optimal AI model for different types of toxicity usually varies, making it essential to conduct comparative analyses of AI methods across toxicity domains. The diverse data sources also pose challenges for researchers focusing on specific toxicity studies. In this review, 10 categories of drug-induced toxicity is examined, summarizing the characteristics and applicable ML models, including both predictive and interpretable algorithms, striking a balance between breadth and depth. Key databases and tools used in toxicity prediction are also highlighted, including toxicology, chemical, multi-omics, and benchmark databases, organized by their focus and function to clarify their roles in drug-induced toxicity prediction. Finally, strategies to turn challenges into opportunities are analyzed and discussed. This review may provide researchers with a valuable reference for understanding and utilizing the available resources to bridge prediction and mechanistic insights, and further advance the application of ML in drugs-induced toxicity prediction.

Molecular Biology and Functions of T Follicular Helper Cells in Cancer and Immunotherapy

T follicular helper (Tfh) cells are integral to the germinal center (GC) response and the development of potent humoral immunity. By priming B cells, Tfh cells can initiate both extrafollicular and GC-dependent Ab responses. The dynamic physical interactions between Tfh and B cells constitute the primary platform for Tfh cells to provide essential "help" factors to B cells, as well as for reciprocal signaling from B cells to sustain the helper state of Tfh cells. In recent years, significant advancements have been made in understanding the diverse roles of Tfh cells across various diseases, particularly in cancer. Notably, beyond the classical GC-Tfh cells, it is increasingly recognized that the Tfh cell phenotype is highly heterogeneous and dynamic, which adds complexity to their roles in disease contexts. This review aims to encapsulate progress in Tfh cell biology, with a focus on their role in cancer and immunotherapy.

Dendritic cell maturation in cancer

Dendritic cells (DCs) are specialized antigen-presenting cells that are present at low abundance in the circulation and tissues; they serve as crucial immune sentinels by continually sampling their environment, migrating to secondary lymphoid organs and shaping adaptive immune responses through antigen presentation. Owing to their ability to orchestrate tolerogenic or immunogenic responses to a specific antigen, DCs have a pivotal role in antitumour immunity and the response to immune checkpoint blockade and other immunotherapeutic approaches. The multifaceted functions of DCs are acquired through a complex, multistage process called maturation. Although the role of inflammatory triggers in driving DC maturation was established decades ago, less is known about DC maturation in non-inflammatory contexts, such as during homeostasis and in cancer. The advent of single-cell technologies has enabled an unbiased, high-dimensional characterization of various DC states, including mature DCs. This approach has clarified the molecular programmes associated with DC maturation and also revealed how cancers exploit these pathways to subvert immune surveillance. In this Review, we discuss the mechanisms by which cancer disrupts DC maturation and highlight emerging therapeutic opportunities to modulate DC states. These insights could inform the development of DC-centric immunotherapies, expanding the arsenal of strategies to enhance antitumour immunity.

Evaluating genetic-ancestry inference from single-cell RNA-seq data

Characterizing the ancestry of donors in single-cell RNA sequencing (scRNA-seq) studies is critical to ensure the genetic homogeneity of the dataset and reduce biases in analyses, to identify ancestry-specific regulatory mechanisms and understand their downstream role in diseases, and to ensure that existing datasets are representative of human genetic diversity. While scRNA-seq is now widely available, the information on the ancestry of the donors is often missing, hindering further analysis. Here we propose a framework to evaluate methods for inferring genetic-ancestry from genetic polymorphisms detected from scRNA-seq reads. We demonstrate that widely used tools (e.g., ADMIXTURE) provide accurate inference of genetic-ancestry and admixture proportions despite the limited number of genetic polymorphisms identified and imperfect variant calling from scRNA-seq reads. We inferred genetic-ancestry for 196 donors from four scRNA-seq datasets from the Human Cell Atlas and highlighted an extremely large proportion of donors of European ancestry. For researchers generating single-cell datasets, we recommend reporting genetic-ancestry inference for all donors and generating datasets that represent diverse ancestries.

Bioinformatic analysis of glycolysis and lactate metabolism genes in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous cancer with significant global incidence. This study investigates glycolysis- and lactate metabolism-related genes (GALMRGs) in HNSCC, focusing on their impact on prognosis, the tumor immune microenvironment, and their potential as therapeutic biomarkers. Analysis of data from the Cancer Genome Atlas and Gene Expression Omnibus identified 16 GALMRGs that were differentially expressed in HNSCC compared to normal tissues. Functional analysis revealed the involvement of lactate and pyruvate metabolism and HIF-1 signaling pathways. Weighted gene co-expression network analysis identified two module genes, CDKN3 and SLC2A1. Five key genes (CAV1, CDKN3, LDHA, MB, and PER2) were identified through univariate, multivariate, and LASSO regression analyses and used to construct a prognostic model. This model demonstrated strong predictive accuracy for overall survival, stratifying patients into high- and low-risk groups. Immune cell infiltration analysis showed a negative correlation between resting and activated mast cells, and low-risk patients had higher tumor mutational burden, suggesting a better response to immunotherapy. Consensus clustering classified HNSCC into two distinct molecular subtypes with differing expression of the key genes. This GALMRG-based prognostic model is a promising biomarker for predicting HNSCC outcomes and immunotherapy responses, providing valuable insights for personalized treatment strategies.

Integrated single-cell and spatial analysis identifies context-dependent myeloid-T cell interactions in head and neck cancer immune checkpoint blockade response

Background

Approximately 15-20% of head and neck cancer squamous cell carcinoma (HNSCC) patients respond favorably to immune checkpoint blockade (ICB). Previous single-cell RNA-Seq (scRNA-Seq) studies identified immune features, including macrophage subset ratios and T-cell subtypes, in HNSCC ICB response. However, the spatial features of HNSCC-infiltrated immune cells in response to ICB treatment need to be better characterized.

Methods

Here, we perform a systematic evaluation of cell interactions between immune cell types within the tumor microenvironment using spatial omics data using complementary techniques from both 10X Visium spot-based spatial transcriptomics and Nanostring CosMx single-cell spatial omics with RNA gene panel including 435 ligands and receptors. In this study, we used integrated bioinformatics analyses to identify cellular neighborhoods of co-localizing cell types in single-cell spatial transcriptomics and proteomics data. In addition, we used both publicly available scRNA-Seq and in-house spatial RNA-Seq data to identify spatially constrained Ligand-Receptor interactions in Responder patients.

Results

With 522,399 single cells profiled with both RNA and protein from 26 patients, in addition to spot-resolved spatial RNA-Seq from 8 patients treated with ICB together with bioinformatics analysis of publicly available single-cell and bulk RNA-Seq, we have identified a spatial and cell-type specific context-dependency of myeloid and T cell interaction difference between Responders and Non-Responders. We defined further cellular neighborhood and the sources of chemokine CXCL9/10-CXCR3 interactions in Responders, emerging targets in ICB, as well as CXCL16-CXCR6, CCL4/5-CCR5, and other underappreciated and potential markers and targets for ICB response in HNSCC. In addition, we have contributed a rich data resource of cell-cell Ligand Receptor interactions for the immunotherapy and HNSCC research community.

Discussion

Our work provides a comprehensive single-cell and spatial atlas of immune cell interactions that correlate with response to ICB in HNSCC. We showcase how integrating multiple technologies and bioinformatics approaches can provide new insights into potential immune-based biomarkers of ICB response. Our results suggested refining future studies using preclinical animal models in a more context-specific manner to elucidate potential underlying mechanisms that lead to improved ICB responses.

Single-cell RNA sequencing reveals an IL1R2+Treg subset driving immunosuppressive microenvironment in HNSCC

Regulatory T cells (Tregs) play an immunosuppressive role in tumor microenvironment (TME) in various of cancer types. However, how different Treg subsets influence and effect on head and neck squamous cell carcinoma (HNSCC) remain unclear. Here, using single-cell RNA sequencing (scRNA-seq), we identified an IL1R2+Treg subset which promoted the progression of HNSCC. Via tissue microassay (TMA) and enzyme-linked immunosorbent assay (ELISA), we verified the clinical diagnostic value of the IL1R2+Treg and soluble IL1R2 (sIL1R2). In addition, we constructed tumor-bearing mouse models to explore the antitumor effects of combined targeting IL1R2 and CTLA4. For mechanism, we found IL-1β promoted the expression of IL1R2 and CTLA4 in Tregs, and upregulated CTLA4 though NR4A1 translocation. These results revealed that IL1R2+Treg and serum IL1R2 level had potential diagnostic and prognostic value of HNSCC and combined targeting of IL1R2 and CTLA4 might be an effective strategy to inhibit tumor progression.

A Single-Cell Transcriptome Atlas of Epithelial Subpopulations in HPV-Positive and HPV-Negative Head and Neck Cancers

Persistent infection with HPV causes nearly 5% of all cancers worldwide, including cervical and oropharyngeal cancers. Compared to HPV-negative (HPV-) head and neck squamous cell carcinomas (HNSCCs), HPV-positive (HPV+) HNSCCs exhibit a significantly improved treatment response; however, established treatment regimens were largely developed for HPV- disease. Effectively de-escalating therapy and optimizing treatment protocols to minimize toxicity for both HPV+ and HPV- tumors has been variably successful, in part due to the heterogeneity of cellular subpopulations. Single-cell RNA sequencing (scRNAseq) has primarily been used to define immune cell populations rather than the cell type of origin, epithelial cells. To address this, we analyzed published scRNAseq data of HPV+ and HPV- HNSCCs to distinguish epithelial tumor cell populations as a function of HPV status. We identified the transcriptome signatures, ontologies, and candidate biomarkers of newly identified epithelial subpopulations with attention to those that are shared or enriched in HPV+ or HPV- HNSCCs. We hypothesize that distinct epithelial cell populations and reprogramming in HPV- versus HPV+ HNSCC represent important components of the pro-tumor environment. These are described here as a foundation for the identification of new epithelial-cell-specific biomarkers, effectors, and candidate targets for optimizing the treatment of HNSCC.

Liquid Biopsy in HPV-Associated Head and Neck Cancer: A Comprehensive Review

Objectives: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer globally, with HPV-positive cases emerging as a distinct subtype with unique clinical and molecular characteristics. Current diagnostic methods, including tissue biopsy and imaging, face limitations in terms of invasiveness, static disease assessment, and difficulty in distinguishing recurrence from treatment-related changes. This review aimed to assess the potential of liquid biopsy as a minimally invasive tool for the diagnosis, treatment monitoring, and surveillance of HPV-associated HNSCC. Methods: This systematic review analyzed literature from PubMed/MEDLINE, Embase, and Web of Science, focusing on original research and reviews related to liquid biopsy applications in HPV-positive HNSCC. Included studies were evaluated based on the robustness of the study design, clinical relevance, and analytical performance of liquid biopsy technologies. Biomarker types, detection methods, and implementation strategies were assessed to identify advancements and challenges in this field. Results: Liquid biopsy technologies, including circulating HPV DNA, ctDNA, and extracellular vesicles, demonstrated high sensitivity (90-95%) and specificity (>98%) in detecting HPV-positive HNSCC. These methods enabled real-time monitoring of tumor dynamics, early detection of recurrence, and insights into treatment resistance. Longitudinal analysis revealed that biomarker clearance during treatment correlates strongly with patient outcomes. Conclusions: Liquid biopsy is a transformative diagnostic and monitoring tool for HPV-associated HNSCC, offering minimally invasive, real-time insights into tumor biology. While challenges remain in standardization and clinical implementation, ongoing research and technological innovations hold promise for integrating liquid biopsy into personalized cancer care, ultimately improving patient outcomes.

Analysis of Head and Neck Cancer scRNA-seq Data Identified PRDM6 Promotes Tumor Progression by Modulating Immune Gene Expression

Head and neck squamous cell carcinoma (HNSCC) is a biologically aggressive and heterogeneous group of cancers with limited treatment options for patients who do not respond to standard therapies. While HPV-related HNSCCs tend to show better therapeutic outcomes, we still had limited understanding of the immune mechanisms underlying these cancers. Immune-responsive genes (IRGs) have emerged as critical factors in regulating both tumor progression and immune response. Recent advances in single-cell RNA sequencing (scRNA-seq) and the development of cell-type specific regulon inference tools, such as IRIS3, have provided new insights into the tumor immune microenvironment. In this study, we leveraged the IRIS3 platform to analyze scRNA-seq data from HNSCC patient samples, identifying novel transcription factor (TF)-IRG networks that contribute to tumor proliferation and immune escape. Specifically, we identified PRDM6, a histone methyltransferase, possesses the previously unknown role in promoting tumor cell proliferation by inducing IRG expression. We further demonstrated that HPV viral oncoproteins (E6/E7) oncoproteins up-regulate the PRDM6 expression, which associates PRDM6 with HPV-positive HNSCC.

A highly resolved integrated single-cell atlas of HPV-negative head and neck cancer

Head and Neck Squamous Cell Carcinomas (HNSCC) are the seventh most prevalent form of cancer and are associated with human papilloma virus infection (HPV-positive) or with tobacco and alcohol use (HPV-negative). HPV-negative HNSCCs have a high recurrence rate, and individual patients' responses to treatment vary greatly due to the high level of cellular heterogeneity of the tumor and its microenvironment. Here, we describe a HNSCC single cell atlas, which we created by integrating six publicly available datasets encompassing over 230,000 cells across 54 patients. We contextualized the relationships between existing signatures and cell populations, identified new subpopulations, and show the power of this large-scale resource to robustly identify associations between transcriptional signatures and clinical phenotypes that would not be possible to discover using fewer patients. We reveal a previously undefined myeloid population, sex-associated changes in cell type proportions, and novel interactions between CXCL8-positive fibroblasts and vascular endothelial cells. Beyond our findings, the atlas will serve as a public resource for the high-resolution characterization of tumor heterogeneity of HPV-negative HNSCC.

Identification of blood-derived exosomal tumor RNA signatures as noninvasive diagnostic biomarkers for multi-cancer: a multi-phase, multi-center study

BACKGROUND

Cancer remains a leading global cause of mortality, making early detection crucial for improving survival outcomes. The study aims to develop a machine learning-enabled blood-derived exosomal RNA profiling platform for multi-cancer detection and localization.

METHODS

In this multi-phase, multi-center study, we analyzed RNA from exosomes derived from peripheral blood plasma in 818 participants across eight cancer types during the discovery phase. Machine learning techniques were applied to identify potential pan-cancer biomarkers. During the screening and model validation phases, the sample size was progressively expanded to 1,385 participants in two steps, while the candidate biomarkers were refined into a set of 12 exosomal tumor RNA signatures (ETR.sig). In the subsequent model construction phase, diagnostic models were developed using the expanded cohort and ETR.sig. Statistical analyses included the calculation of receiver operating characteristic (ROC) curves and AUC values to assess the models' ability to distinguish cancer cases from controls and determine tumor origins. To further validate and explore the biological relevance of the identified biomarkers, we integrated tissue RNA-seq, single-cell data, and clinical information.

RESULTS

Machine learning analysis initially identified 33 candidate biomarkers, which were narrowed down to 20 ETR.sig in the screening phase and 12 ETR.sig in the validation phase. In the model construction phase, a diagnostic model based on ETR.sig, built using the Random Forest (RF) algorithm, showed excellent performance with an AUC of 0.915 for distinguishing pan-cancer from controls. The multi-class classification model also demonstrated strong classification power, with macro-average and micro-average AUCs of 0.983 and 0.985, respectively, for differentiating between eight cancer types. Additionally, tumor origin classification using the RF-based diagnostic models achieved high AUC values: BRCA 0.976, COAD 0.98, KIRC 0.947, LIHC 0.967, LUAD 0.853, OV 0.972, PAAD 0.977, and PRAD 0.898. Integration of tissue RNA-seq, single-cell data, and clinical information revealed key associations between ETR.sig-related genes and tumor development.

CONCLUSIONS

The study demonstrates the robust potential of exosomal RNA as a minimally invasive biomarker resource for cancer detection. The developed ETR.sig platform offers a promising tool for precision oncology and broad-spectrum cancer screening, integrating advanced computational models with nanoscale vesicle biology for accurate and rapid diagnosis.

Analyze the Diversity and Function of Immune Cells in the Tumor Microenvironment From the Perspective of Single-Cell RNA Sequencing

BACKGROUND

Cancer development is closely associated with complex alterations in the tumor microenvironment (TME). Among these, immune cells within the TME play a huge role in personalized tumor diagnosis and treatment.

OBJECTIVES

This review aims to summarize the diversity of immune cells in the TME, their impact on patient prognosis and treatment response, and the contributions of single-cell RNA sequencing (scRNA-seq) in understanding their functional heterogeneity.

METHODS

We analyzed recent studies utilizing scRNA-seq to investigate immune cell populations in the TME, focusing on their interactions and regulatory mechanisms.

RESULTS

ScRNA-seq reveals the functional heterogeneity of immune cells, enhances our understanding of their role in tumor antibody responses, and facilitates the construction of immune cell interaction networks. These insights provide guidance for the development of cancer immunotherapies and personalized treatment approaches.

CONCLUSION

Applying scRNA-seq to immune cell analysis in the TME offers a novel pathway for personalized cancer treatment. Despite its promise, several challenges remain, highlighting the need for further advancements to fully integrate scRNA-seq into clinical applications.

Tumor and blood B-cell abundance outperforms established immune checkpoint blockade response prediction signatures in head and neck cancer

BACKGROUND

Immunotherapy has improved the outcomes for some patients with head and neck squamous-cell carcinoma (HNSCC). However, the low and variable response rates observed highlight the need for robust response biomarkers to select patients for treatment.

PATIENTS AND METHODS

We assembled and analyzed a large HNSCC dataset, encompassing 11 clinical cohorts including 1232 patient samples, spanning a variety of disease subtypes and immune checkpoint blockade (ICB) treatment types, tissue sources, data modalities, and timing of measurements. We conducted a comprehensive evaluation of the predictive power of various cell types, traditional biomarkers, and emerging predictors in both blood and tumor tissues of HNSCC patients.

RESULTS

Tumor B-cell infiltration emerged as a strong and robust predictor of both patient survival and ICB response. It outperformed all other established biomarkers of response to ICB, including the tertiary lymphoid structure signature and numerous T-cell-based signatures. B-cell infiltration was associated with a 'hot' antitumor microenvironment that promotes tumor eradication. Furthermore, B-cell levels in peripheral blood mononuclear cells (PBMCs) correlated strongly with tumor B-cell levels and demonstrated high predictive value for ICB response, with high odds ratios (≥7.8) in two independent clinical cohorts.

CONCLUSION

B-cell abundance, whether assessed in PBMCs or tumor tissues, is one of the strongest predictors of ICB response in HNSCC. For translation to patient care, measuring B-cell abundance in PBMCs via cytometry offers a practical and accessible tool for clinical decision making.

Dysfunctional CD11c-CD21- extrafollicular memory B cells are enriched in the periphery and tumors of patients with cancer

Many patients with recurrent and metastatic cancer fail to produce a durable response to immunotherapy, highlighting the need for additional therapeutic targets to improve the immune landscape in tumors. Recent studies have highlighted the importance of B cells in the antitumor response, with memory B cells (MBCs) being prognostic in a variety of solid tumors. MBCs are a heterogenous B cell subset and can be generated through both germinal center reactions and extrafollicular (EF) responses. EF-derived MBCs have been recently linked to poor prognosis and treatment resistance in solid tumors and thus may represent candidate biomarkers or immunotherapy targets. EF-derived MBCs, termed "double-negative" (DN) MBCs may be further classified on the basis of surface expression of CD11c and CD21 into DN1, DN2, and DN3 MBCs. CD11c-CD21+ DN1 MBCs and CD11c+CD21- DN2 MBCs have been well studied across inflammatory diseases; however, the biology and clinical relevance of CD11c-CD21- DN3 MBCs remain unknown. Here, we report an accumulation of DN3 MBCs in the blood and tumors of patients with head and neck squamous cell carcinoma (HNSCC) and an increase in DN3 MBCs in locally advanced HNSCC tumors. Circulating and intratumoral DN3 MBCs were hyporesponsive to antigen stimulation, had low antibody production, and failed to differentiate into antibody-secreting cells. Moreover, DN3 MBCs accumulated selectively outside of tertiary lymphoid structures. Last, circulating DN3 MBCs correlated with poor therapeutic response, advanced disease, and worse outcomes in patients with HNSCC and melanoma, supporting further assessment of EF-derived MBCs as potential biomarkers and therapeutic targets.

Does a Transcriptionally Active HPV Infection Affect the Invasiveness of Pituitary Neuroendocrine Tumors? A Case Series Study of 60 Patients in Krakow, Poland

BACKGROUND/OBJECTIVE

Pituitary neuroendocrine tumors (PITNETs) often show a tendency towards invasive behavior, i.e., an invasion towards the cavernous sinuses or destruction of the sella turcica. In the present study, we analyzed whether a transcriptionally active HPV infection affects the invasiveness of pituitary tumors.

METHODS

Sixty patients with different phenotypes of PITNETs who underwent neurosurgery were studied. The obtained postoperative material was analyzed histopathologically. For each patient, formalin-fixed paraffin-embedded blocks were cut into ultra-thin slices and two to three of them were designated for DNA extraction, while one was used for histological slides. Based on the isolated DNA, the presence of DNA from individual HPV types was determined by the real-time detection polymerase chain reaction using the REALQUALITY RQ-Multi HPV Detection reagent kit (AB ANALITICA, Italy). P16 protein expression was assessed by immunohistochemical staining on the histological slides. A transcriptionally active infection with individual HPV types was distinguished when HPV DNA and P16 protein overexpression were detected simultaneously for a given tumor.

RESULTS

In the group of the 60 analyzed PITNETs, a transcriptionally active high-risk HPV infection was detected in a subset of 11 tumors (18.3%). This infection was associated with a significantly lower probability of tumor invasiveness, measured on both the Knosp (OR = 0.11, 95% CI: 0.02-0.58) and Hardy scales (OR = 0.12 95% CI: 0.024-0.56).

CONCLUSIONS

Further studies are needed to confirm the prevalence of transcriptionally active HPV infections in pituitary adenomas and the role of these infections in the invasiveness of pituitary tumors.

B cells in non-lymphoid tissues

B cells have long been understood to be drivers of both humoral and cellular immunity. Recent advances underscore this importance but also indicate that in infection, inflammatory disease and cancer, B cells function directly at sites of inflammation and form tissue-resident memory populations. The spatial organization and cellular niches of tissue B cells have profound effects on their function and on disease outcome, as well as on patient response to therapy. Here we review the role of B cells in peripheral tissues in homeostasis and disease, and discuss the newly identified cellular and molecular signals that are involved in regulating their activity. We integrate emerging data from multi-omic human studies with experimental models to propose a framework for B cell function in tissue inflammation and homeostasis.

New advances in the therapeutic strategy of head and neck squamous cell carcinoma: A review of latest therapies and cutting-edge research

Head and neck squamous cell carcinoma (HNSCC) is a common and aggressive malignancy with a poor prognosis, particularly when diagnosed at advanced stages. Despite progress in surgical, chemotherapeutic, and radiotherapeutic interventions, the five-year survival rate remains low due to high rates of recurrence and therapeutic resistance. This review explores recent advances in therapeutic strategies for HNSCC, focusing on targeted therapies, immunotherapy, and innovative drug delivery systems. Targeted therapies, such as EGFR inhibitors and PI3K/AKT/mTOR pathway inhibitors, offer promising options for overcoming HNSCC, though resistance challenges persist. Emerging treatments, including dual-target inhibitors and personalized therapeutic approaches, show potential in addressing these limitations. Immunotherapy, particularly PD-1/PD-L1 blockade, has achieved positive outcomes in a subset of patients, though overall response rates remain modest. Strategies aimed at enhancing immune responses, such as combination therapies and nanotechnology-based drug delivery systems, are actively being investigated to improve efficacy. This review also underscores the critical role of the tumor microenvironment and epithelial-mesenchymal transition (EMT) in HNSCC progression and therapeutic resistance. Novel approaches, including smart drug delivery systems utilizing nanotechnology and immune modulation, are opening new avenues for more personalized and effective treatments. Ongoing interdisciplinary research into molecular targets and advanced drug delivery techniques holds great promise for significantly improving patient outcomes in HNSCC.

Investigating the Impact of B Cell-Related Genes on Colorectal Cancer Immunosuppressive Environment and Immunotherapy Evasion

We aimed to elucidate the prognostic and immunological roles of B cell-related genes in colorectal cancer (CRC). This study comprehensively integrated data from single-cell RNA-sequencing, TCGA, GEO, IMvigor210, GDSC, CancerSEA, HPA, and TISIDB databases to explore prognostic implications and immunological significance of B cell-related gene signature in CRC. We identified seven prognostically significant B cell-related genes for constructing a risk score. Clinical relevance analysis indicated that this risk score served as an independent prognostic factor, with the model accurately predicting patient outcomes. GSEA results implicated the risk score in immune function, cell cycle, and DNA replication. Immune infiltration analysis revealing lower levels of B cells, CD4+ cells, and CD8+ cells in the high-risk group, correlating with decreased immune activity and function. IMvigor210 and TIDE analysis indicated poorer prognosis among high-risk group patients receiving immune therapy. Additionally, the high-risk group exhibited lower sensitivity to immune therapy. Further analysis of drug sensitivity suggested higher resistance to common chemotherapy drugs among high-risk groups. Finally, we identified HSPA1A as the gene with the strongest association with immune and inflammatory responses. Validation of HSPA1A protein expression and prognosis demonstrated elevated expression in CRC compared to normal colorectal tissue, further reinforcing its association with poorer prognosis and higher tumor stage. The risk score exhibited substantial variations in clinical characteristics, functional mechanism, TMB, drug sensitivity, immune cell infiltration, and immune subtype. Our findings may aid in clinical decision-making by shedding light on novel and promising biomarkers for CRC prognosis and immunotherapy response prediction.

The prognostic significance of tertiary lymphoid structures in oral squamous cell carcinomas: a systematic review

Introduction

Upper aerodigestive tract cancers are prevalent, with a global incidence surpassing 500,000 new cases in 2018. Among these, oral squamous cell carcinomas (OSCC) constitute the majority. OSCC has a low 5-year survival rate due to late-stage diagnosis. Risk factors include alcohol and tobacco use. However, non-smokers and non-drinkers are also affected, especially young patients with tongue cancer. The impact of tumor microenvironment (TME) and tumor-infiltrating lymphocytes (TILs) on OSCC prognosis remains debated. Remarkably, Tertiary Lymphoid Structures (TLS) identified in solid tumors have shown associations with favorable outcomes, yet their prognostic significance in OSCC remains understudied.

Objective

Thus, this systematic review aims to explore the value of TLS in OSCC reported in the literature.

Method

A scoping review was conducted and six retrospective cohort studies involving 1,203 patients met the inclusion criteria.

Results

Predominantly male patients, with an average age of 49.3 years were included. Immunohistochemistry was the primary method to identify TLS, present in 21% up to 100% of cases. TLS were predominantly located in the peri-tumoral area (75.4%-84.8%) compared to the intra-tumoral area (33.8%-33.9%). Our review shows that the presence of TLS is associated with improved survival in OSCC.

Discussion

However, variations in TLS detection and classification methods across studies introduce potential biases, hindering direct comparisons between findings. For instance, reports that are based solely on examining HES-stained slides for TLS identification may raise reliability concerns. Standardization of methodologies is imperative to ensure consistency in criteria utilization, thereby facilitating meaningful data comparisons.

Systematic Review Registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023428010, PROSPERO (CRD42023428010).

The Single-Cell Landscape of Peripheral and Tumor-infiltrating Immune Cells in HPV- HNSCC

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. HPV-negative HNSCC, which arises in the upper airway mucosa, is particularly aggressive, with nearly half of patients succumbing to the disease within five years and limited response to immune checkpoint inhibitors compared to other cancers. There is a need to further explore the complex immune landscape in HPV-negative HNSCC to identify potential therapeutic targets. Here, we integrated two single-cell RNA sequencing datasets from 29 samples and nearly 300,000 immune cells to investigate immune cell dynamics across tumor progression and lymph node metastasis. Notable shifts toward adaptative immune cell populations were observed in the 14 distinct HNSCC-associated peripheral blood mononuclear (PBMCs) and 21 tumor-infiltrating immune cells (TICs) considering disease stages. All PBMCs and TICs revealed unique molecular signatures correlating with lymph node involvement; however, broadly, TICs increased ligand expression among effector cytokines, growth factors, and interferon-related genes. Pathway analysis comparing PBMCs and TICs further confirmed active cell signaling among Monocyte-Macrophage, Dendritic cell, Natural Killer (NK), and T cell populations. Receptor-ligand analysis revealed significant communication patterns shifts among TICs, between CD8+ T cells and NK cells, showing heightened immunosuppressive signaling that correlated with disease progression. In locally invasive HPV-negative HNSCC samples, highly multiplexed immunofluorescence assays highlighted peri-tumoral clustering of exhausted CD8+ T and NK cells, alongside their exclusion from intra-tumoral niches. These findings emphasize cytotoxic immune cells as valuable biomarkers and therapeutic targets, shedding light on the mechanisms by which the HNSCC sustainably evades immune responses.

Tertiary lymphoid structures and cancer immunotherapy: From bench to bedside

Tertiary lymphoid structures (TLSs) are organized ectopic lymphoid aggregates within the tumor microenvironment that serve as crucial sites for the development of adaptive antitumor cellular and humoral immunity. TLSs have been consistently documented in numerous cancer types, correlating with improved prognosis and enhanced responses to immunotherapy, especially immune-checkpoint blockade (ICB). Given the potential role of TLSs as predictive biomarkers for the efficacy of ICB in cancer patients, the therapeutic manipulation of TLSs is gaining significant attention as a promising avenue for cancer treatment. Herein, we comprehensively review the composition, definition, and detection methods of TLSs in humans. We also discuss the contributions of TLSs to antitumor immunity, their prognostic value in cancer patients, and their association with therapeutic response to ICB-based immunotherapy. Finally, we present preclinical data supporting the potential of therapeutically manipulating TLSs as a promising approach for innovative cancer immunotherapy.

Nationwide multi-centric prospective study for the identification of biomarkers to predict the treatment responses of nivolumab through comprehensive analyses of pretreatment plasma exosome mRNAs from head and neck cancer patients (BIONEXT study)

Background

Nivolumab paved a new way in the treatment of patients with recurrent or metastatic (RM) head and neck squamous cell carcinoma (RM-HNSCC). However, the limited rates of long-term survivors (< 20%) demand a robust prognostic biomarker. This nationwide multi-centric prospective study aimed to identify a plasma exosome (PEX) mRNA signature, which serves as a companion diagnostic of nivolumab and provides a biological clue to develop effective therapies for a majority of non-survivors.

Methods

Pre-treatment plasmas (N = 104) of RM-HNSCC patients were subjected to comprehensive PEX mRNA analyses for prognostic marker discovery and validation. In parallel, paired treatment-naïve tumor and plasma samples (N = 20) were assayed to elucidate biological implications of the PEX mRNA signature.

Results

Assays for pre-treatment blood samples (N = 104) demonstrated that a combination of 6 candidate PEX mRNAs plus neutrophil-to-lymphocyte ratio precisely distinguished non-survivors from >2-year survivors (2-year OS; 0% vs 57.7%; P = 0.000124) with a high hazard ratio of 2.878 (95% CI 1.639-5.055; P = 0.0002348). Parallel biological assays demonstrated that in the paired treatment-naïve HNSCC tumor and plasma samples (N = 20), PEX HLA-E mRNA (a non-survivor-predicting marker) was positively corelated with overexpression of HLA-E protein (P = 0.0191) and the dense population of tumor-infiltrating NK cells (P = 0.024) in the corresponding tumor, suggesting that the HLA-E-NKG2A immune checkpoint may inhibit the antitumor effect of PD-1blockade.

Conclusion

The PEX mRNA signature could be useful as a companion diagnostic of nivolumab. The combination of an anti-NKG2A antibody (i.e., monalizumab) and nivolumab may serve as a treatment option for non-survivors predicted by a RT-qPCR-based pre-treatment measurement of PEX mRNAs.

Divergent response to radio-immunotherapy is defined by intrinsic features of the tumor microenvironment

BACKGROUND

Treatment with immunotherapy can elicit varying responses across cancer types, and the mechanistic underpinnings that contribute to response vrsus progression remain poorly understood. However, to date there are few preclinical models that accurately represent these disparate disease scenarios.

METHODS

Using combinatorial radio-immunotherapy consisting of PD-1 blockade, IL2Rβγ biased signaling, and OX40 agonism we were able to generate preclinical tumor models with conflicting responses, where head and neck squamous cell carcinoma (HNSCC) models respond and pancreatic ductal adenocarcinoma (PDAC) progresses.

RESULTS

By modeling these disparate states, we find that regulatory T cells (Tregs) are expanded in PDAC tumors undergoing treatment, constraining tumor reactive CD8 T cell activity. Consequently, the depletion of Tregs restores the therapeutic efficacy of our treatment and abrogates the disparity between models. Moreover, we show that through heterotopic implantations the site of tumor development defines the response to therapy, as implantation of HNSCC tumors into the pancreas resulted in comparable levels of tumor progression.

CONCLUSIONS

This work highlights the complexity of combining immunotherapies within the tumor microenvironment (TME) and further defines the immune and non-immune components of the TME as an intrinsic feature of immune suppression.

Differential impact of TIM-3 ligands on NK cell function

BACKGROUND

The transmembrane protein T-cell immunoglobulin and mucin-domain containing molecule 3 (TIM-3) is an immune checkpoint receptor that is expressed by a variety of leukocyte subsets, particularly in the tumor microenvironment. An effective TIM-3-targeting therapy should account for multiple biological factors, including the disease setting, the specific cell types involved and their varying sensitivities to the four putative TIM-3 ligands (galectin-9, phosphatidylserine, high mobility group protein B1 and carcinoembryonic antigen cell adhesion molecule 1), each of which engages a unique binding site on the receptor's variable immunoglobulin domain. The primary objectives of this study were to assess the prevalence and function of TIM-3+ natural killer (NK) cells in patients with head and neck squamous cell carcinoma (HNSCC), determine whether the four TIM-3 ligands differentially affect TIM-3+ NK cell functions, identify the most immunosuppressive ligand, and evaluate whether targeting ligand-mediated TIM-3 signaling enhances NK cell effector functions.

METHODS

Single-cell RNA sequencing and flow cytometry were used to study the prevalence, phenotypes and function of TIM-3+ NK cells in HNSCC patient tumors and blood. In vitro killing, proliferation and cytokine production assays were implemented to evaluate whether the four TIM-3 ligands differentially modulate TIM-3+ NK cell functions, and whether disruption of TIM-3/ligand interaction can enhance NK cell-mediated antitumor effector mechanisms. Finally, The Cancer Genome Atlas survival analysis and digital spatial profiling were employed to study the potential impact of etiology-associated differences on patients with HNSCC outcomes.

RESULTS

We demonstrate that TIM-3 is highly prevalent on circulating and tumor-infiltrating NK cells. It co-expresses with CD44 and marks NK cells with heightened effector potential. Among the four putative TIM-3 ligands, galectin-9 most consistently suppresses NK cell-mediated cytotoxicity and proliferation through TIM-3 and CD44 signaling, respectively, but promotes IFN-γ release in a TIM-3-dependent manner. Among patients with HNSCC, an elevated intratumoral TIM-3+ NK cell gene signature associates with worse outcomes, specifically in those with human papillomavirus (HPV)+ disease, potentially attributable to higher galectin-9 levels in HPV+ versus HPV- patients.

CONCLUSIONS

Our findings underscore the complex functional impact of TIM-3 ligand signaling, which is consistent with recent clinical trials suggesting that targeting TIM-3 alone is suboptimal as an immunotherapeutic approach for treating malignancies.

Type I Interferon Drives a Cellular State Inert to TCR-Stimulation and Could Impede Effective T-Cell Differentiation in Cancer

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) is linked to human papillomavirus (HPV) infection. HPV-positive and HPV-negative HNSCC exhibit distinct molecular and clinical characteristics. Although checkpoint inhibitors have shown efficiency in recurrent/metastatic HNSCC, response variability persists regardless of HPV status. This study aimed to explore the CD8+ T-cell landscape in HPV-negative HNSCC.

METHODS

We performed simultaneous single-cell RNA and TCR sequencing of CD8+ tumor-infiltrating lymphocytes (TILs) from treatment-naïve HPV-negative HNSCC patients. Additionally, cells were stimulated ex vivo, which allowed for the tracking of clonal transcriptomic responses.

RESULTS

Our analysis identified a subset of CD8+ TILs highly enriched for interferon-stimulated genes (ISG). TCR analysis revealed ISG cells are clonally related to a population of granzyme K (GZMK)-expressing cells. However, unlike GZMK cells, which exhibited rapid effector-like phenotypes following stimulation, ISG cells were transcriptionally inert. Additionally, ISG cells showed specific enrichment within tumor and were found across multiple tumor entities.

CONCLUSIONS

ISG-enriched CD8+ TILs are a consistent feature of various tumor entities. These cells are poorly understood but possess characteristics that may impact antitumor immunity. Understanding the unique properties and functionality of ISG cells could offer innovative treatment approaches to improve patient outcomes in HPV-negative HNSCC and other cancer types.

Integrated machine learning to predict the prognosis of lung adenocarcinoma patients based on SARS-COV-2 and lung adenocarcinoma crosstalk genes

Viruses are widely recognized to be intricately associated with both solid and hematological malignancies in humans. The primary goal of this research is to elucidate the interplay of genes between SARS-CoV-2 infection and lung adenocarcinoma (LUAD), with a preliminary investigation into their clinical significance and underlying molecular mechanisms. Transcriptome data for SARS-CoV-2 infection and LUAD were sourced from public databases. Differentially expressed genes (DEGs) associated with SARS-CoV-2 infection were identified and subsequently overlapped with TCGA-LUAD DEGs to discern the crosstalk genes (CGs). In addition, CGs pertaining to both diseases were further refined using LUAD TCGA and GEO datasets. Univariate Cox regression was conducted to identify genes associated with LUAD prognosis, and these genes were subsequently incorporated into the construction of a prognosis signature using 10 different machine learning algorithms. Additional investigations, including tumor mutation burden assessment, TME landscape, immunotherapy response assessment, as well as analysis of sensitivity to antitumor drugs, were also undertaken. We discovered the risk stratification based on the prognostic signature revealed that the low-risk group demonstrated superior clinical outcomes (p < 0.001). Gene set enrichment analysis results predominantly exhibited enrichment in pathways related to cell cycle. Our analyses also indicated that the low-risk group displayed elevated levels of infiltration by immunocytes (p < 0.001) and superior immunotherapy response (p < 0.001). In our study, we reveal a close association between CGs and the immune microenvironment of LUAD. This provides preliminary insight for further exploring the mechanism and interaction between the two diseases.

The combined use of scRNA-seq and network propagation highlights key features of pan-cancer Tumor-Infiltrating T cells

Improving the selectivity and effectiveness of drugs represents a crucial issue for future therapeutic developments in immuno-oncology. Traditional bulk transcriptomics faces limitations in this context for the early phase of target discovery as resulting gene expression levels represent the average measure from multiple cell populations. Alternatively, single cell RNA sequencing can dive into unique cell populations transcriptome, facilitating the identification of specific targets. Here, we generated Tumor-Infiltrating regulatory T cells (TI-Tregs) and exhausted T cells (Tex) gene signatures from a single cell RNA-seq pan-cancer T cell atlas. To overcome noise and sparsity inherent to single cell transcriptomics, we then propagated the gene signatures by diffusion in a protein-protein interaction network using the Patrimony high-throughput computing platform. This methodology enabled the refining of signatures by rescoring genes based on their biological connectivity and shed light not only on processes characteristics of TI-Treg and Tex development and functions but also on their immunometabolic specificities. The combined use of single cell transcriptomics and network propagation may thus represent an innovative and effective methodology for the characterization of cell populations of interest and eventually the development of new therapeutic strategies in immuno-oncology.

The Display between HPV Infection and Host Immunity in Cervical Cancer

Most cervical cancers are related to the persistent infections of high-risk Human Papillomavirus (HPV) infections. Increasing evidence has witnessed the immunosuppressive effectiveness of HPV in the oncogenesis steps and progression steps. Here we review the immune response in HPV-related cervical malignancies and discuss the crosstalk between HPVs and the host immune response. Furthermore, we describe the identification and development of current immunotherapies in cervical cancer. Above all, we hope to provide a novel insight of the display between HPV infections and the host immune system.

Aging and head and neck cancer insights from single cell and spatial transcriptomic analyses

BACKGROUND

Head and neck squamous cell carcinoma(HNSCC) is the sixth most common malignancy worldwide, with more than 890,000 new cases and 450,000 deaths annually. Its major risk factors include smoking, alcohol abuse, aging, and poor oral hygiene. Due to the lack of early and effective detection and screening methods, many patients are diagnosed at advanced stages with a five-year survival rate of less than 50%. In this study, we deeply explored the expression of Aging-related genes(ARGs) in HNSCC and analyzed their prognostic significance using single-cell sequencing and spatial transcriptomics analysis. This research aims to provide new theoretical support and directions for personalized treatment. Annually, more than 890,000 new cases of head and neck squamous cell carcinoma (HNSCC) are diagnosed globally, leading to 450,000 deaths, making it the sixth most common malignancy worldwide. The primary risk factors for HNSCC include smoking, alcohol abuse, aging, and poor oral hygiene. Many patients are diagnosed at advanced stages due to the absence of early and effective detection and screening methods, resulting in a five-year survival rate of less than 50%. In this research, single cell sequencing and spatial transcriptome analysis were used to investigate the expression of Aging-related genes (ARGs) in HNSCC and to analyse their prognostic significance. This research aims to provide new theoretical support and directions for personalized treatment.

METHODS

In this study, we investigated the association between HNSCC and AGRs by utilizing the GSE139324 series in the GEO database alongside the TCGA database, combined with single-cell sequencing and spatial transcriptomics analysis. The data were analyzed using Seurat and tSNE tools to reveal intercellular communication networks. For the spatial transcriptome data, SCTransform and RunPCA were applied to examine the metabolic activities of the cells. Gene expression differences were determined through spacerxr and RCTD tools, while the limma package was employed to identify differentially expressed genes and to predict recurrence rates using Cox regression analysis and column line plots. These findings underscore the potential importance of molecular classification, prognostic assessment, and personalized treatment of HNSCC.

RESULTS

This study utilized HNSCC single-cell sequencing data to highlight the significance of ARGs in the onset and prognosis of HNSCC. It revealed that the proportion of monocytes and macrophages increased, while the proportion of B cells decreased. Notably, high expression of the APOE gene in monocytes was closely associated with patient prognosis. Additionally, a Cox regression model was developed based on GSTP1 and age to provide personalized prediction tools for clinical use in predicting patient survival.

CONCLUSIONS

We utilized single-cell sequencing and spatial transcriptomics to explore the cellular characteristics of HNSCC and its interaction with the tumor microenvironment. Our findings reveal that HNSCC tissues show increased mononuclear cells and demonstrate enhanced activity in ARGs, thereby advancing our understanding of HNSCC development mechanisms.

Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives

BACKGROUND

Identifying differentially expressed genes (DEGs) is a core task of transcriptome analysis, as DEGs can reveal the molecular mechanisms underlying biological processes. However, interpreting the biological significance of large DEG lists is challenging. Currently, gene ontology, pathway enrichment and protein-protein interaction analysis are common strategies employed by biologists. Additionally, emerging analytical strategies/approaches (such as network module analysis, knowledge graph, drug repurposing, cell marker discovery, trajectory analysis, and cell communication analysis) have been proposed. Despite these advances, comprehensive guidelines for systematically and thoroughly mining the biological information within DEGs remain lacking.

AIM OF REVIEW

This review aims to provide an overview of essential concepts and methodologies for the biological interpretation of DEGs, enhancing the contextual understanding. It also addresses the current limitations and future perspectives of these approaches, highlighting their broad applications in deciphering the molecular mechanism of complex diseases and phenotypes. To assist users in extracting insights from extensive datasets, especially various DEG lists, we developed DEGMiner (https://www.ciblab.net/DEGMiner/), which integrates over 300 easily accessible databases and tools.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review offers strong support and guidance for exploring DEGs, and also will accelerate the discovery of hidden biological insights within genomes.

Dysfunction of exhausted T cells is enforced by MCT11-mediated lactate metabolism

CD8+ T cells are critical mediators of antitumor immunity but differentiate into a dysfunctional state, known as T cell exhaustion, after persistent T cell receptor stimulation in the tumor microenvironment (TME). Exhausted T (Tex) cells are characterized by upregulation of coinhibitory molecules and reduced polyfunctionality. T cells in the TME experience an immunosuppressive metabolic environment via reduced levels of nutrients and oxygen and a buildup of lactic acid. Here we show that terminally Tex cells uniquely upregulate Slc16a11, which encodes monocarboxylate transporter 11 (MCT11). Conditional deletion of MCT11 in T cells reduced lactic acid uptake by Tex cells and improved their effector function. Targeting MCT11 with an antibody reduced lactate uptake specifically in Tex cells, which, when used therapeutically in tumor-bearing mice, resulted in reduced tumor growth. These data support a model in which Tex cells upregulate MCT11, rendering them sensitive to lactic acid present at high levels in the TME.

Immune checkpoint expression on tumor-infiltrating lymphocytes (TIL) is dependent on HPV status in oropharyngeal carcinoma (OPSCC) - A single-cell RNA sequencing analysis

INTRODUCTION

A substantial proportion of head and neck squamous cell carcinoma (HNSCC), particularly oropharyngeal squamous cell carcinoma (OPSCC), is associated with human papillomavirus (HPV), resulting in distinct molecular phenotypes. In this study, we investigated differential immune checkpoint molecule (ICM) expression by HPV status using RNA sequencing data to identify additional ICM targets that may complement anti-PD1 antibodies.

MATERIAL AND METHODS

RNA sequencing was performed on 51 OPSCC cases and validated using the TCGA HNSCC dataset. Unsupervised clustering and differential gene expression analyses in R were conducted based on HPV status. Additionally, a published single-cell RNA sequencing (scRNA) dataset of tumor-infiltrating lymphocytes (TIL) and peripheral immune cells (PBMC) (GSE139324) was analyzed with a Seurat pipeline grouped by HPV status.

RESULTS

Our study identified a significant upregulation of all examined ICM in HPV-positive OPSCC through bulk RNA sequencing, validated by the TCGA cohort. Unsupervised clustering revealed a strong association between HPV-positive/-negative and high/low ICM expression cases respectively, indicating overlap between ICM and HPV status. In scRNA analysis, CD27, PD-1, OX-40, and BTLA were significantly more highly expressed on TILs of HPV-positive OPSCC. Conversely, VSIR was increased in PBMC and TILs of HPV-negative OPSCC, while LAG3 expression on PBMC was reduced in HPV-negative OPSCC.

CONCLUSION

Our study unveils the intricate interplay of ICMs in OPSCC, emphasizing the necessity for personalized therapeutic approaches based on HPV status and immune profiles. The identified ICMs, including PD1, CD27, and CTLA4, are promising candidates for further investigation and may enhance immunotherapeutic interventions in the HPV-dependent treatment strategies for OPSCC.

IL-12 drives the expression of the inhibitory receptor NKG2A on human tumor-reactive CD8 T cells

Blockade of NKG2A/HLA-E interaction is a promising strategy to unleash the anti-tumor response. Yet the role of NKG2A+ CD8 T cells in the anti-tumor response and the regulation of NKG2A expression on human tumor-infiltrating T cells are still poorly understood. Here, by performing CITE-seq on T cells derived from head and neck squamous cell carcinoma and colorectal cancer, we show that NKG2A expression is induced on CD8 T cells differentiating into cytotoxic, CD39+CD103+ double positive (DP) cells, a phenotype associated with tumor-reactive T cells. This developmental trajectory leads to TCR repertoire overlap between the NKG2A- and NKG2A+ DP CD8 T cells, suggesting shared antigen specificities. Mechanistically, IL-12 is essential for the expression of NKG2A on CD8 T cells in a CD40/CD40L- dependent manner, in conjunction with TCR stimulation. Our study thus reveals that NKG2A is induced by IL-12 on human tumor-reactive CD8 T cells exposed to a TGF-β-rich environment, highlighting an underappreciated immuno-regulatory feedback loop dependent on IL-12 stimulation.

Morphine treatment restricts response to immunotherapy in oral squamous cell carcinoma

BACKGROUND

Immune checkpoint inhibitors (ICIs) are becoming the standard of care for recurrent and metastatic cancer. Opioids, the primary treatment for cancer-related pain, are immunosuppressive raising concerns about their potential to interfere with the efficacy of ICIs. We hypothesize that exogenous opioids given for analgesia suppress antitumor immunity via T cell-mediated mu opioid receptor 1 (OPRM1) signaling.

METHODS

In silico bioinformatics were used to assess OPRM1 receptor expression on tumor-infiltrating immune cells in patients with head and neck squamous cell carcinoma (HNSCC) and across different cancer types. A syngeneic orthotopic mouse model of oral squamous cell carcinoma was used to study the impact of morphine and OPRM1 antagonism on tumor-infiltrating immune cells, tumor growth and antitumor efficacy of anti-Programmed cell death protein 1 (PD-1) monoclonal antibody treatment.

RESULTS

In patients with HNSCC, OPRM1 expression was most abundant in CD8+ T cells, particularly in patients who had not been prescribed opioids prior to resection and exhibited increased expression of exhaustion markers. Exogenous morphine treatment in tumor-bearing mice reduced CD4+ and CD8+ T-cell infiltration and subsequently anti-PD1 ICI efficacy. Peripherally acting mu opioid receptor antagonism, when administered in the adjunctive setting, was able to block morphine-induced immunosuppression and recover the antitumor efficacy of anti-PD1.

CONCLUSIONS

These findings suggest that morphine acts via a peripheral OPRM1-mediated mechanism to suppress CD8+ T cells, thereby fostering a pro-tumor-impaired immune response. Importantly, peripherally-restricted OPRM1 antagonism can effectively block this morphine-induced immunosuppression while still allowing for centrally-mediated analgesia, indicating a potential therapeutic strategy for mitigating the adverse effects of opioid pain relief in cancer treatment.

Research trends, hotspots and future directions of tertiary lymphoid structures in cancer: a comprehensive informatics analysis and visualization study

Many studies have reported the presence of tertiary lymphoid structures (TLSs) in cancer, but the research progress of TLSs in cancer has not been systematically analyzed. Therefore, we analyzed the global scientific knowledge in the field using informatics methods. The results showed that TLSs in cancer have received increasing attention since the 21st century, with an annual publication growth rate of 27.86%. Unsupervised hierarchical clustering based on machine learning further categorized the research features into four clusters, with the cluster related to immunotherapy being considered an emerging cluster. TLSs and immunotherapy were identified as the top two hotspots with the highest occurrence frequency and total link strength. The Walktrap algorithm indicated that "TLSs, carcinoma, prognostic value" and "high endothelial venules, germinal-centers, node-like structures" are important to TLSs but remain underexplored, representing promising research directions. These findings suggest that cancer-related TLSs have brought new insights into antitumor immunity, and targeting TLSs has the potential to transform the landscape of antitumor immunotherapy.

Association of B cells and the risk of Esophageal cancer: a bidirectional two-sample mendelian randomization study

BACKGROUND AND OBJECTIVES

Currently, research on the role of B cells in esophageal cancer (EC) is limited, and existing studies on their impact are controversial. Therefore, this study was conducted to elucidate the complex causal relationship between B cells and EC, expand the understanding of esophageal cancer immunology.

METHODS

Bidirectional two-sample Mendelian randomization (MR) was performed to assess the causal relationships between 190 B cell phenotypes and EC. To complement the MR analysis, Bayesian Weighted Mendelian Randomization (BWMR) was employed, and sensitivity analyses were conducted to evaluate the robustness of the findings. Positive results were further validated in independent cohorts of esophageal cancer studies. In addition, RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) were utilized for validation, incorporating B cell-related gene expression analysis and functional enrichment analysis to support the MR findings.

RESULTS

In the primary analysis, significant causal relationships were observed between 5 B cell types and the risk of EC; the onset of EC was causally linked to 3 B cell phenotypes. Validation in other cohorts revealed that 4 outcomes aligned with the primary analysis, included were CD19 on IgD + CD38-, CD20 on IgD- CD27-, CD20 on IgD- CD38br, and CD38 on PB/PC. Further validation using RNA-seq data showed that CD38 mRNA was significantly overexpressed in EC tissues, whereas CD19 and MS4A1 mRNA levels did not differ significantly between tumor and normal tissues. Functional enrichment analysis revealed that CD19, MS4A1, and CD38 are involved in multiple tumor-related immune pathways, suggesting their pivotal role in regulating the tumor immune microenvironment.

CONCLUSIONS

Our study suggests a potential connection between B cell phenotypes and EC through bidirectional two-sample MR combined with BWMR analysis, providing a preliminary basis for future research.